Báo cáo khoa học: Targeting mechanism of the retinoblastoma tumor suppressor by a prototypical viral oncoprotein Structural modularity, intrinsic disorder and phosphorylation of human papillomavirus E7 doc
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Targetingmechanismoftheretinoblastoma tumor
suppressor byaprototypicalviral oncoprotein
Structural modularity,intrinsicdisorderandphosphorylation of
human papillomavirus E7
Lucı
´
a B. Chemes, Ignacio E. Sa
´
nchez, Clara Smal and Gonzalo de Prat-Gay
Protein Structure-Function and Engineering Laboratory, Fundacio
´
n Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
Keywords
LxCxE motif; natively unfolded proteins;
phosphorylation; retinoblastoma protein;
viral oncoprotein
Correspondence
Gonzalo de Prat-Gay, Protein Structure-
Function and Engineering Laboratory,
Fundacio
´
n Instituto Leloir and
IIBBA-CONICET, Av. Patricias Argentinas
435, 1405 Buenos Aires, Argentina
Fax: +54 11 5238 7501
Tel: +54 11 5238 7500 ext. 3209
E-mail: gpg@leloir.org.ar
(Received 16 November 2009, revised 4
December 2009, accepted 7 December
2009)
doi:10.1111/j.1742-4658.2009.07540.x
DNA tumor viruses ensure genome amplification by hijacking the cellular
replication machinery and forcing infected cells to enter the S phase. The
retinoblastoma (Rb) protein controls the G1 ⁄ S checkpoint, and is targeted
by several viral oncoproteins, among these theE7 protein from human
papillomaviruses (HPVs). A quantitative investigation ofthe interaction
mechanism between the HPV16 E7 protein andthe RbAB domain in solu-
tion revealed that 90% ofthe binding energy is determined bythe LxCxE
motif, with an additional binding determinant (1.0 kcalÆmol
)1
) located
in the C-terminal domain of E7, establishing a dual-contact mode. The
stoichiometry and subnanomolar affinity ofE7 indicated that it can
bind RbAB as a monomer. The low-risk HPV11 E7 protein bound 2.0
kcalÆmol
)1
more weakly than the high-risk HPV16 and HPV18 type
counterparts, but the modularity and binding mode were conserved. Phos-
phorylation at a conserved casein kinase II site in the natively unfolded
N-terminal domain ofE7 affected the local conformation by increasing the
polyproline II content and stabilizing an extended conformation, which
allowed for a tighter interaction with the Rb protein. Thus, the E7–RbAB
interaction involves multiple motifs within the N-terminal domain of E7
and at least two conserved interaction surfaces in RbAB. We discussed a
mechanistic model ofthe interaction ofthe Rb protein with aviral target
in solution, integrated with structural data andthe analysis of other cellu-
lar andviral proteins, which provided information about the balance of
interactions involving the Rb protein and how these determine the progres-
sion into either the normal cell cycle or transformation.
Structured digital abstract
l
MINT-7383794, MINT-7383812, MINT-7383830, MINT-7383868, MINT-7383891, MINT-
7384056: E7 (uniprotkb:P03129) and Rb (uniprotkb:P06400) bind (MI:0407)byfluorescence
technologies (
MI:0051)
l
MINT-7383923: E7 (uniprotkb:P04020) and Rb (uniprotkb:P06400) bind (MI:0407)bycom-
petition binding (
MI:0405)
Abbreviations
AdE1A, adenovirus E1A; BPVN, N-terminal fragment ofthe BPV1 E7 protein; CKII, casein kinase II; CR1, conserved region 1; CR2,
conserved region 2; CtIP, transcriptional corepressor CtBP-interacting protein; E7(16-40)PP, a synthetic E7(16-40) peptide phosphorylated at
serine residues 31 and 32; FITC, fluorescein isothiocyanate; GST, glutathione S-transferase; HDAC, histone deacetylase; HPV, human
papillomavirus; IPTG, isopropyl thio-b-
D-galactoside; MBP, maltose-binding protein; PII, polyproline type II; Rb, retinoblastoma; SV40LT, SV40
large T antigen; TA, transactivation region; TFE, 1,1,1, trifluoroethanol.
FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS 973
Introduction
The retinoblastomatumorsuppressor gene (RB1) was
first identified as the causative agent whose loss
resulted in retinoblastoma, a heritable disease of pedi-
atric relevance [1]. To date, over 500 distinct muta-
tions in the RB1 gene have been identified in
retinoblastoma tumors, 50 of which are missense
mutations [2,3]. Thetumorsuppressor function of the
Rb protein is underscored by its mutation in a broad
range ofhuman tumors [4]. The most extensively
studied function ofthe Rb protein is in the control
of cell cycle progression at the G1 ⁄ S boundary, medi-
ated through its interaction with the E2F family of
transcription factors [5]. The Rb protein also plays
important roles in chromatin remodeling, develop-
ment, differentiation and apoptosis [6]. These multiple
functions are mediated by over 100 interactions with
different protein partners that are dependent on the
cell type, and on the developmental and cell cycle
stages [7].
The Rb protein has a molecular mass of 105 kDa
and is composed of three domains. Both the N-terminal
and the AB (RbAB) domains consist ofa double cyclin
fold [8,9], while the C-terminal domain (RbC) appears
to be natively unfolded [10]. The function ofthe N-ter-
minal domain is still poorly defined. The RbAB domain
mediates transcriptional repression and, together with
the C-terminal domain (RbC), promotes growth arrest
[11,12]. Most interacting partners contact more than
one structural domain in the Rb protein [13–15]. For
example, the ‘transactivation’ domain of E2F (E2F-TA)
binds to RbAB, whereas the ‘marked box’ domain
(E2F-MB) binds to RbC [10,16]. Moreover, there are at
least two distinct highly conserved ligand-binding sites
within the RbAB domain [8] (Figs 1 and S1). Cellular
proteins containing an LxCxE motif interact with a site
located on the B subdomain of RbAB [8,17]
(Fig. 1A,B). The E2F-TA domains bind to a site
located at the cleft between theAand B subdomains on
the opposite side of RbAB [16,18] (Fig. 1C,D).
Early evidence for thetumorsuppressor role of the
Rb protein came from themechanismof action of the
human papillomavirus (HPV) E7 major transforming
protein [19]. The interaction between E7andthe Rb
protein is required for the induction and maintenance
of the transformed state ofhuman keratinocytes [20].
Deregulation ofE7 expression upon integration of the
HPV genome is believed to play a role in HPV-medi-
ated oncogenesis. The DNA tumor virus proteins
SV40 large T antigen (SV40LT) and adenovirus E1A
(AdE1A) also target the Rb protein and share
sequence and functional conservation with the HPV
E7 protein [21,22]. E7, AdE1A and SV40LT each con-
tain several functional andstructural domains, each of
which mediates interactions with different cellular tar-
gets. The three transforming proteins share conserved
region 2 (CR2); E7and AdE1A also share conserved
region 1 (CR1).
E7 is a small ($ 100 amino acids) protein composed
of two structural domains. We have previously deter-
mined that the N-terminal domain (E7N) is natively
unfolded [23,24], includes CR1 and CR2, and contains
dynamic elements of helical and polyproline type II
(PII) secondary structure [23]. The globular C-terminal
domain (E7C) constitutes conserved region 3 (CR3)
and is responsible for protein dimerization and zinc
binding [24,25] (Fig. 2A). While the CR1 and CR2
domains are required for Rb protein degradation, all
conserved E7 regions participate in transformation
[26,27]. E7 can also oligomerize in vitro and in vivo
[28–30]. The conformational diversity ofE7 may be an
evolved trait that allows for multiple modes of pro-
tein–protein interaction [31,32].
E7 binds to two structural domains in the Rb
protein, namely the RbAB and RbC domains. Binding
to both domains is required for E2F displacement [33].
The LxCxE motif within the CR2 region of E7
mediates high-affinity binding to the RbAB domain
[8,34] (Fig. 1A), while the isolated E7C binds to the
RbC domain with micromolar affinity [25,35]. The
crystal structure ofthe LxCxE–RbAB complex reveals
that the motif binds to a conserved shallow groove of
the B subdomain in an extended conformation
(Fig. 1A). The LxCxE motif is followed in E7 CR2 by
two conserved serine residues (S31 and S32) andby a
l
MINT-7383777, MINT-7384078, MINT-7383848, MINT-7384113, MINT-7384096: Rb (uni-
protkb:
P06400) andE7 (uniprotkb:P03129) bind (MI:0407)bycompetition binding (MI:0405)
l
MINT-7383963: Rb (uniprotkb:P06400) andE7 (uniprotkb:P06788) bind (MI:0407)bycom-
petition binding (
MI:0405)
l
MINT-7384022, MINT-7384040: E7 (uniprotkb:P03129) and Rb (uniprotkb:P06400) bind
(
MI:0407)bycomigration in non denaturing gel electrophoresis (MI:0404)
l
MINT-7384004, MINT-7383984: Rb (uniprotkb:P06400) binds (MI:0407)toE7 (uni-
protkb:
P03129)bypull down (MI:0096)
Viral targetingoftheretinoblastoma protein L. B. Chemes et al.
974 FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS
stretch of acidic amino acids, and HPV16 E7 is
phosphorylated at S31 and S32 by casein kinase II
(CKII) in vitro and in vivo [36,37]. Phosphorylation is
required for E7 function, and cell culture assays have
suggested that phosphorylation modulates the strength
of the E7–RbAB interaction, but this proposal remains
a matter of debate [37–40].
Indirect evidence suggests that other regions in E7
may contribute to binding to the RbAB domain. For
example, mutagenesis ofa conserved surface patch in
the A subdomain ofthe RbAB domain (Fig. 1A,B,
right) produces a protein capable of arresting the cell
cycle of HeLa cells, implying that this protein was resis-
tant to E7 inactivation [41]. It is currently unclear
whether E7 interacts directly with this surface. Similarly,
an E7 construct, encompassing the CR2 and CR3
domains of E7, bound to the RbAB domain more
tightly than a CR2 construct and was able to debilitate
the E2F–RbAB interaction [16]. Finally, E7 CR1 has
been shown to contribute to E2F displacement in com-
bination with CR2 [27]. This E7 region shares a high
degree of sequence similarity to the AdE1A CR1 region
and can functionally complement it [42]. The AdE1A
CR1 region binds to the RbAB domain at a site that
overlaps with the E2F-TA-binding site [43] (Fig. 1D),
leading to disruption ofthe E2F–Rb complex, but an
interaction between E7 CR1 andthe RbAB domain has
not been demonstrated to date.
Mechanistic aspects and structure–function relation-
ships for the Rb protein remain ill defined [17], in con-
trast to those for other well-known tumor suppressors
or oncogenes, such as p53 [44] or Ras [45]. A complete
understanding ofthe Rb protein function requires the
dissection of all functional surfaces, along with their
partners andthe strength andmechanismof interac-
tion [46]. We have dissected individual contact sites
and their energetic contribution to the E7–RbAB com-
plex, using solution-based measurements of binding
affinity at equilibrium. This mechanistic and thermody-
namic picture ofthe complex formed by RbAB and
E7 paves the way for a better understanding ofthe Rb
cellular complexes that control the cell cycle through-
out eukaryotes and their deregulation in HPV infection
and oncogenesis.
Results
Quantitative dissection ofthe E7–RbAB
interaction in solution
The minimal region required for the interaction
between the HPV16 E7 protein andthe RbAB pocket
has previously been mapped to residues 21-29 of E7,
A
B
C
D
Fig. 1. Conserved surface features ofthe RbAB domain. Conserva-
tion scores were calculated using the alignment ofthe RbAB domain
from 46 vertebrate species and
CONSURF [74], and figures were gen-
erated using
PYMOL [75]. Structures correspond to the following com-
plexes: (A) RbAB ⁄ E7 (PDB ID: 1GUX); (B) RbAB ⁄ SV40-LT (PDB ID:
1GH6); (C) RbAB ⁄ E2F-TA (PDB ID: 1N4M); and (D) RbAB ⁄ E1A-CR1
(PDB ID: 2R7G). Asterisk: H549Y missense mutation [54]. Arrows
indicate the rotation ofthe molecule along the x-axis between two
consecutive images. The color scale indicates the residue conserva-
tion score, as calculated using the
CONSURF algorithm.
L. B. Chemes et al. Viraltargetingoftheretinoblastoma protein
FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS 975
containing the LxCxE motif [8]. The dissociation con-
stant for this interaction was shown, by isothermal
titration calorimetry, to be 190 nm [8,34], but the con-
tribution of other regions oftheE7 protein to the
affinity ofthe E7–RbAB complex has not been
explored in detail. In order to address this issue, we
developed a solution-based assay that allowed us to
perform quantitative and accurate determinations of
stoichiometry and binding affinity at equilibrium, by
measuring the fluorescence anisotropy change upon the
binding of fluorescein isothiocyanate (FITC)-labeled
E7 fragments to RbAB. This assay was used to mea-
sure the binding of different fragments ofE7 (corre-
sponding to well-defined structuraland functional
domains and to highly conserved sequence motifs) to
RbAB. Figure 2A shows theE7 regions tested.
A representative example ofthe assay is presented in
Fig. 2B,C, which show the association of E7N [E7(1-
40)] with RbAB. First, the stoichiometry ofthe reac-
tions was determined by performing titrations at a
high peptide concentration (Figs 2B and S2). The
anisotropy signal increased linearly up to a 1 : 1 molar
ratio, where it reached a constant value indicating the
saturation of all binding sites. This implies that there
is one binding site for the E7(1-40) peptide per RbAB
monomer and that the stoichiometry ofthe E7(1-40)–
RbAB interaction is 1 : 1. Far-UV CD spectra of the
complexes formed by binding ofthe RbAB domain to
full-length E7, and to E7(1-40) and E7(40-98) peptides,
revealed that formation ofthe complex does not
induce significant structural changes in the secondary
structure ofthe interacting proteins (data not shown).
Figure 2C shows one representative binding curve per-
formed at substoichiometric concentrations, and the
residuals ofthe fit from which the K
D
value was calcu-
lated. We tested the association ofthe RbAB domain
with a 43-residue N-terminal fragment ofthe BPV1 E7
protein (BPVN), which does not contain an LxCxE
motif. This interaction had marginal affinity, which
was approximately 10
6
times lower than that of the
full-length E7 protein (Table 1). Figure 2D summarizes
all binding curves and shows the dynamic range of the
assay, which allowed us to accurately determine subn-
anomolar to micromolar dissociation constants.
The E7(21-29) peptide, comprising the minimal
LxCxE motif (DLYCYEQLN) [8], associated with
RbAB with a K
D
of 4.7 ± 1.7 nm (Table 1), and the
free energy of binding for this interaction was DG =
A
BCD
Fig. 2. Interaction of different E7 fragments with the RbAB domain. (A) Scheme of HPV16 E7. The positions of conserved regions 1, 2 and
3 (CR1, CR2 and CR3) andtheE7 fragments used in this study are shown; the LxCxE motif is underlined. Boxes denote the regions con-
tained in each fragment: black, LxCxE motif; dark grey, CKII ⁄ PEST motif; light grey, CR1 helix-forming residues. Circles denote the position
of FITC moieties. (B) Association of E7(1-40) and RbAB at 200 n
M E7(1-40). (C) Association of E7(1-40) andthe RbAB domain at 5 nM E7(1-
40). A fit to a 1 : 1 binding model and residuals are shown. The anisotropy value ofthe free peptide was 0.054 ± 0.001 andthe anisotropy
of the complex was 0.124 ± 0.001, indicating that no oligomerization occurred in this binding regime [76]. (D) Representative normalized
binding curves for the different E7 fragments (symbols are as shown in panel A).
Viral targetingoftheretinoblastoma protein L. B. Chemes et al.
976 FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS
)11.2 ± 0.2 kcalÆmol
)1
. The E7(16-31) and E7(16-40)
peptides, which contain the LxCxE motif plus addi-
tional neighboring sequences from the CR2 region,
and the E7(1-40) peptide, which comprises both CR1
and CR2, had the same affinity for the RbAB domain
as the E7(21-29) peptide (Table 1). The full-length
HPV16 E7 protein bound to the RbAB domain with a
ten-fold increased affinity when compared with the
E7(21-29) peptide (K
D
= 0.6 ± 0.3 nm), andthe free
energy of binding for the interaction between full-
length E7andthe RbAB domain was DG = )12.4 ±
0.3 kcalÆmol
)1
(Table 1). Therefore, our data show
that the LxCxE motif contributes about 90% of the
total binding energy for the HPV16 E7–RbAB interac-
tion, providing quantitative support to previous results
[47]. The CR1 region does not appear to contribute to
RbAB binding within the context of an E7N mono-
mer, as shown bythe fact that the E7(16-40) and
E7(1-40) peptides have the same affinity for the RbAB
domain (Table 1). Finally, we showed that the E7
C-terminal domain contributes 1.0 ± 0.4 kcalÆmol
)1
to
the total free energy of binding, enhancing the affinity
of the E7–RbAB complex by ten-fold.
Previous semiquantitative assays have established
that E7 proteins from HPV types highly associated
with the development of cervical cancer (HPV16 and
HPV18) bind to the full-length Rb protein more
strongly than E7 proteins from HPV types associated
with benign lesions (HPV11 and HPV6) [48]. In order
to explore whether similar regions determine the
affinity for RbAB in E7 proteins from high-risk and
low-risk HPV types, we used a competition assay to
measure the association between the RbAB domain
and theE7 proteins from HPV types 16, 18 and 11.
We assembled a stoichiometric complex of RbAB and
FITC-labeled HPV16 E7 or E7(16-31) and displaced
labeled E7 with each ofthe different full-length pro-
teins or N-terminal domains (Fig. 3A and Table 2).
The HPV11 E7 protein associated with the RbAB
domain 2.0 kcalÆmol
)1
more weakly than the high-risk
HPV16 and HPV18 type counterparts, providing quan-
titative support to previous reports [48]. The N-termi-
nal domain was the main contributor to the binding
affinity ofE7 from HPV11, HPV16 and HPV18 for
the RbAB domain (Fig. 3B), pointing to a conserved
mode of interaction.
Phosphorylation ofthe conserved CKII sites
within theE7 CR2 region increases affinity for
RbAB
The sequences C-terminal to the LxCxE motif in
HPV16 E7 contain two serine residues, S31 and S32,
which are phosphorylated in vitro and in vivo by CKII
[36,37]. These serine residues are followed bya stretch
of acidic amino acids that constitute an S ⁄ TxxD ⁄ E
CKII consensus site. The PESTfind algorithm suggests
Table 1. Determination of binding affinities for the E7–RbAB
complex. The K
D
was calculated by fitting three to five independent
binding curves to a 1 : 1 binding model, as described in the Materials
and methods.
Fragment K
D
(nM) DG
a
(kcalÆmol
)1
)
E7
b
0.6 ± 0.3 )12.4 ± 0.3
E7(21-29) (LXCXE)
b
4.7 ± 1.7 )11.2 ± 0.2
E7(16-31) (LXCXE)
b
5.1 ± 1.3 )11.1 ± 0.3
E7(16-40) (CR2)
b
6.5 ± 1.0 )11.0 ± 0.3
E7(16-40)PP (CR2PP)
b
1.8 ± 0.4 )11.7 ± 0.1
E7(1-40) (E7N)
b
3.0 ± 1.6 )11.4 ± 0.3
E7(1-20) (CR1) 19000 ± 2000 )6.3 ± 0.1
E7(40-98) (E7C) 2700 ± 600 )7.5 ± 0.1
BPV(1-43) (BPV-N) > 400 000 –
a
DG was calculated as DG = )RT *ln(K
D
), with RT = 0.582
kcalÆmol
)1
.
b
The stoichiometry for these complexes was deter-
mined to be 1 : 1 by titrations performed at peptide concentrations
at least 10 times greater than the determined K
D
.
A
B
Fig. 3. The LxCxE motif is the main determinant of binding affinity
in HPV-E7 proteins. (A) Competition experiments with full-length
E7 proteins anda preformed complex of 5 n
M RbAB and 5 nM
FITC-HPV16-E7 protein. Competitor proteins were: BPV-Nter (s);
HPV11-E7 (
); HPV18-E7 ( ); and HPV16-E7 (d). (B) Comparison
of DG values for different E7 full-length proteins (solid bars) and
N-terminal domains (hatched bars). Data are from Table 2.
L. B. Chemes et al. Viraltargetingoftheretinoblastoma protein
FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS 977
that this site overlaps with a PEST degradation motif
[49]. Figure 4A shows the sequence ofthe HPV16 E7
CR2 region, indicating the relative positions of the
LxCxE motif, the phosphorylatable serine residues and
the CKII ⁄ PEST region within CR2. Aligned below this
sequence is a sequence logo created from the alignment
of all 56 E7 proteins from genital HPV types (Fig. S3).
The sequence logo clearly shows that serine residues
are nearly as conserved as the LxCxE motif. Inspection
of individual sequences revealed that all 56 E7 proteins
present at least one CKII consensus site between
positions 30 and 34. This region also contained a high
proportion of negatively charged amino acids (D⁄ E),
with 97% of sequences presenting a net charge that
was equal to or lower than -6.
The striking conservation of sequence features
within the CR2 region ofE7 underscores the impor-
tance of this region for E7-mediated transformation.
The CKII ⁄ PEST region ofE7and its phosphorylation
have been postulated to play a role in the E7–Rb
protein interaction. Here, we directly tested this
hypothesis by comparing binding to the RbAB domain
for E7(16-40) and for a synthetic E7(16-40) peptide
phosphorylated at serine residues 31 and 32 [E7(16-
40)PP]. Phosphorylation increased the affinity four-
fold (Table 1). The difference in free energy of binding
of both peptides, DDG = )0.7 ± 0.3 kcalÆmol
)1
, was
significant across repeated assays. We further validated
the data by carrying out competition experiments,
where a stoichiometric complex of FITC-labeled
E7(16-31) andthe RbAB domain was titrated with
increasing amounts of unlabeled E7(16-40) or E7(16-
40)PP peptides. Competition experiments (Fig. 4B,C)
confirmed a positive contribution of phosphorylation
to RbAB-binding affinity. The difference in free
A
BC
Fig. 4. PhosphorylationoftheE7 CR2 region increases the affinity for the RbAB domain. (A) Conservation of sequence features within E7
CR2. Upper panel: sequence ofthe HPV16 E7(16-40) peptide. The LxCxE motif is underlined, andthe position of phosphoryl serine residues
and the CKII ⁄ PEST consensus are marked. Lower panel: sequence logo ofthe CR2 region from genital E7 proteins. The height ofthe stack
of letters at each position denotes the level of conservation (the maximum value is 4.32), while the relative proportions of each residue rep-
resents the relative abundance. (B) Competition experiments with CR2 peptides anda preformed complex of 25 n
M RbAB andthe 25 nM
FITC–E7(16-31) peptide. Competitor peptides were: E7(16-31) (d), E7(16-40) (.), E7(16-40)PP (s) and BPVN ()). (C) Comparison of DG val-
ues for the E7(16-40) and E7(16-40)PP peptides with those for the E7(16-31) peptide. Data are from Table 1 and from panel B.
Table 2. The LxCxE motif determines binding affinity in distantly
related HPV E7 proteins.
Fragment K
D
(nM) DG
a
(kcalÆmol
)1
) DDG
b
(kcalÆmol
)1
)
Full-length protein
HPV16 E7 2.4 ± 0.2 )11.6 ± 0.05 –
HPV18 E7 7.8 ± 0.5 )10.9 ± 0.04 0.7 ± 0.06
HPV11 E7 108 ± 5 )9.3 ± 0.03 2.3 ± 0.06
N-terminal domain
HPV16 E7 8.6 ± 1.3 )10.8 ± 0.09 –
HPV18 E7 12.2 ± 0.8 )10.6 ± 0.04 0.2 ± 0.1
HPV11 E7 366 ± 25 )8.6 ± 0.04 2.2 ± 0.1
a
DG = )RT*ln(K
D
), with RT = 0.582 kcalÆmol
)1
.
b
DDG was calcu-
lated as DDG = DG ) DG
E716
.
Viral targetingoftheretinoblastoma protein L. B. Chemes et al.
978 FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS
energy of binding from competition experiments was
DDG = )1.4 ± 0.2 kcalÆmol
)1
, in agreement with
the direct binding data. Our data demonstrated that
phosphorylation ofthe CKII ⁄ PEST region contributes
significantly to the RbAB–E7 interaction, enhancing
the affinity by fourfold to 10-fold.
Structural correlates ofE7phosphorylation at the
CKII sites
We have previously shown that E7N is an extended bona
fide structural domain, with regions of dynamic residual
secondary structure in solution. Far-UV CD analyses
showed that HPV16 E7(1-40) displayed an extended PII
structure, which was stabilized byphosphorylation of
serine residues S31 and S32 [23]. We tested theE7 CR2
region for PII content by measuring the far-UV CD
spectra ofthe E7(16-40) andthe E7(16-40)PP peptides
at 5 °C. Both peptides presented a CD spectrum charac-
teristic for a disordered polypeptide with a positive band
at 218 nm, which is characteristic ofthe PII conforma-
tion (Fig. 5A). PII conformations are sensitive to tem-
perature, with higher temperatures decreasing the
intensity ofthe 218 and 198 nm peaks. Increasing the
temperature to 85 °C decreased the intensity of both
peaks for both peptides, characteristic for the disruption
of the PII structure (Fig. 5A). The difference spectra (5–
85 °C) clearly showed the induction at 5 °C of the
218 nm peak (Fig. 5A, inset). The denaturant GdmCl is
known to stabilize PII structures [50]. We have previ-
ously shown that the stability of PII conformations can
be estimated from GdmCl titrations, by validating
changes in the CD spectra with NMR measurements of
PII structure [51]. GdmCl increased the 218 nm band in
the E7(16-40)PP peptide, but not in the E7(16-40) pep-
tide (Fig. 5B), suggesting that the E7(16-40)PP peptide
has a higher propensity for PII structure. The titration
of the E7(16-40)PP peptide with GdmCl is shown in
Fig. 5C, along with a fit ofthe data to a two-state coil-
PII model. The calculated free energy for the coil-PII
equilibrium in 0 m GdmCl is 1.7 ± 0.7 kcalÆmol
)1
,
which corresponds to 4.6 ± 6% ofthe PII population
in the absence of denaturant. Although the model used
is a crude estimate ofthe true conformational equilibria
of the peptide, andthe estimated parameters have high
errors as a result of noise in the measurements, the
GdmCl titration data clearly show that the E7(16-40)PP
peptide is in equilibrium between coil and PII conforma-
tions. Overall, our data indicate that both peptides from
the HPV16 E7 CR2 region present residual PII structure
in equilibrium with disordered conformations. GdmCl
titrations strongly suggest that phosphorylation modu-
lates the coil–PII equilibrium, increasing the PII propen-
sity oftheE7 CR2 region.
The E7 C-terminal domain binds independently
to RbAB
The increased affinity ofthe full-length E7 protein
compared with theE7 N-terminal domain suggested
that additional regions within theE7 C-terminal
domain contribute to association with the RbAB
domain. In order to test for a direct interaction
between E7C and RbAB, we performed a pull-down
assay with recombinant purified proteins by forming a
stoichiometric complex of His-tagged RbAB with E7
and E7C (Fig. 6A). Most ofthe full-length E7 protein
(96%), anda fraction oftheE7 C-terminal domain
(23%), bound to RbAB at a concentration of 10 lm.
These results confirmed a direct association of the
RbAB domain with both E7and E7C, and suggested
that the E7C–RbAB interaction was weaker than the
Fig. 5. Phosphorylation increases the PII content oftheE7 CR2 region. (A) Far-UV CD spectra ofthe E7(16-40) (solid line) andthe E7(16-
40)PP (dashed line) peptides, performed at 5 °C and 85 °C. Inset: difference spectra (5–85 °C) for the E7(16-40) (solid line) andthe E7(16-
40)PP (dashed line) peptides. (B) CD spectra of E7(16-40) and E7(16-40)PP between 0 and 6
M GdmCl. Titration points graphed are
[GdmCl] = 0, 1.2, 1.9, 2.4, 3.2, 3.7, 4.9 and 5.9
M. The curves corresponding to 0 and 5.9 M GdmCl are shown in bold. (C) GdmCl titration of
the E7(16-40)PP peptide. Data were fit to a two-state coil-PII equilibrium (DG
H2O
E7(16-40)PP
= 1.7 ± 0.7 kcalÆmol
)1
; m = 0.44 ± 0.22 kcal
mol
)1
ÆM
)1
).
L. B. Chemes et al. Viraltargetingoftheretinoblastoma protein
FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS 979
interaction ofthe full-length E7 protein with the
RbAB domain. Direct titration showed that the E7C–
RbAB complex had a dissociation constant of
2.7 ± 0.6 lm (Table 1, Fig. 6B). Titration with BPVN
E7 yielded a dissociation constant of 400 lm or higher,
supporting the specificity ofthe E7C–RbAB interac-
tion. A peptide containing the CR2 region ofE7 did
not compete with E7C binding, indicating that E7C
does not bind to the RbAB domain at the LxCxE-
binding cleft (Table 1, Fig. 6B).
The E7 CR1 region can form an alpha helix and
binds independently to RbAB
The CR1 region from E1A binds to the RbAB domain
with micromolar affinity (K
D
=1lm) [43] at the
interface between theAand B subdomains, which is
also the binding site for E2F-TA (Fig. 1C,D). The fact
that theE7and AdE1A CR1 regions have similar
functional properties [42] suggests that E7 CR1 might
also bind to the RbAB domain at the E2F-TA-binding
site.
E1A CR1 and E2F-TA form a six-residue helix in
the bound conformation (Fig. 1C, residues boxed in
Fig. 7A) [16,18,43]. Four AdE1A residues that estab-
lish intermolecular contacts with the RbAB domain
(P41, L43, H44 and L49), and two residues that stabi-
lize the helix by an intramolecular hydrogen bond
(T42 and E45) [43], are conserved in E7 CR1 (E7
residues 6-10 and 15; Fig. 7A). Furthermore, the
AGADIR algorithm [52] suggests that E7 residues 6 to
15 have local helical propensity (data not shown). We
tested whether theE7 CR1 region could form an
a-helix in solution by measuring the far-UV CD spec-
trum of E7(1-20) in the presence of 1,1,1, trifluoroetha-
nol (TFE), which is known to stabilize helical
conformations in peptides [53]. The addition of 60%
TFE induced an a-helix structure in E7(1-20) (Fig. 7B
and inset). A fit ofthe TFE titration data to a two-
state coil-helix model yielded a free energy for a-helix
formation in 0% TFE of 1.3 ± 0.2 kcalÆmol
)1
, corre-
sponding to a residual a-helix population of 10 ± 4%
in the absence of cosolvent. These results show that
the E7and E1A CR1 regions have similar conforma-
tional properties.
We tested for the association between E7 CR1 and
the RbAB domain using three different approaches.
First, we used nondenaturing PAGE and FITC-labeled
E7 peptides to test for complex formation (Fig. 7C).
As a positive control, we tested the association
between FITC-labeled E7(1-40) andthe RbAB
domain, and as a test for the specificity ofthe interac-
tion, we used ovalbumin in place of RbAB. Both
E7(1-40) and E7(1-20) formed a complex with RbAB
but not with the control protein ovalbumin, confirming
the specificity ofthe interactions (Fig. 7C). A pull-
down assay, similar to that performed with E7C, did
not show significant interaction (data not shown), sug-
gesting that the E7(1-20)–RbAB complex has a lower
affinity than the E7C–RbAB complex. Fluorescence
titration gives a dissociation constant of 19 ± 1 lm
for the E7(1-20)–RbAB complex (Fig. 7D and
Table 1). Titration with BPVN yielded a dissociation
constant of 400 lm or higher. The 20-fold higher affin-
ity for the E7(1-20)–RbAB complex supports the speci-
ficity ofthe interaction. Peptides containing the CR2
region did not compete for the E7(1-20)–RbAB inter-
action (Fig. 7C), which indicates that E7(1-20) does
not bind RbAB at the LxCxE-binding site.
A
B
Fig. 6. E7C binds independently to the RbAB domain. (A)
Pull-down assay for the RbAB–E7C interaction. His-RbAB was incu-
bated with E7 (lanes 3-4) or with E7C (lanes 7-8). Lanes 1-2 and
5-6: control experiments excluding His-RbAB. The labels to the left
of the gel indicate the position of each protein. % E7: percentage
of E7 or E7C protein in the bound (B) and unbound (U) fractions, as
quantified by densitometry (see the Materials and methods). (B)
Binding of E7C to the RbAB domain in solution. Titrations were per-
formed at 1 l
M FITC-E7C; the titrant was RbAB (d, K
D
= 4.8 ± 0.5
l
M), RbAB-E7(16-40) (s, K
D
= 6.4 ± 0.9 lM). A control experiment
was performed using 5 l
M FITC-BPVN (4, K
D
> 400 lM).
Viral targetingoftheretinoblastoma protein L. B. Chemes et al.
980 FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS
Discussion
Despite its vast importance as the guardian ofthe cell
cycle and its clinical relevance in human cancers, struc-
tural and thermodynamic understanding ofthe mecha-
nisms of action ofthe Rb protein is far behind that of
p53, the keeper ofthe genome, mutated in most can-
cers and targeted bythe same DNA tumor viruses that
target the Rb protein [44]. In this work, we set out to
investigate the interaction mechanismofthe RbAB
pocket domain with one ofthe paradigmatic viral
oncoproteins, HPV E7, which targets it for degrada-
tion. Precise quantitative assessment of Rb protein
interactions is fundamental for understanding viral-
mediated subversion of cell cycle control and allows
novel shared features ofviraland cellular Rb protein
interaction partners to be uncovered.
We measured the contribution ofthe LxCxE motif
of E7 to be 90% ofthe total binding free-energy, and
showed that this motif is also the main determinant of
binding for E7 proteins from three prototypical HPV
types (Figs 2 and 3). The free energy of binding for
full-length HPV16 E7 was 1.0 kcalÆmol
)1
higher than
that ofthe E7N domain, revealing that the E7C
domain contributes a 10-fold increase in affinity
through a dual-contact mode of interaction. Careful
examination of conserved surface patches in the RbAB
domain suggests a putative binding site for E7C,
located in the RbA domain close to the AB cleft (Rb
residues E492, F514, P515, K548 and H549; Fig. 1A,B,
right). This site is nearly as conserved as the LxCxE
cleft, the lysine-rich patch andthe E2F-binding site [8],
and a tumorigenic missense mutation, H549Y, has
been described at this surface (Fig. 1A,B, asterisk)
[3,54], which strongly suggests that this is an important
functional surface in the RbAB domain for which
cellular binding partners are likely to be described in
the future [7]. Mutations in this region affect cell cycle
regulation byE7 [41], suggesting that E7 may bind at
this interaction site and displace Rb protein cellular
targets.
The viral transforming proteins AdE1A and
SV40LT, in addition to nine cellular protein targets of
Rb [17] [histone deacetylase (HDAC)1, HDAC2, tran-
scriptional corepressor CtBP-interacting protein (CtIP),
95kDa retinoblastoma-associated protein (RBP95),
ETS-related transcription factor 1 (Elf1), HMG Box
transcription factor 1 (HBP1), kinetochore protein
Hec1 (Hec1), RBP1 and replication factor C subunit 1
(RFC1)], present a putative serine-phosphorylation site
following the LxCxE motif (Fig. 8). In addition, in vivo
phosphorylation ofthe AdE1A, SV40-LT and HDAC
sites has functional consequences [55–57]. In HPV E7,
A
B
C
D
Fig. 7. TheE7 CR1 region forms an a-helix and interacts with the
RbAB domain. (A) Alignment oftheE7 CR1 region with the E1A CR1
and E2F1-TA RbAB-binding sites. Bold: residues in AdE1A involved in
complex formation with RbAB and conserved in E7. Asterisks: resi-
dues of E1A and E2F1 involved in the RbAB-binding a-helix [16,43].
(B) TFE titration ofthe E7(1-20) peptide. Data were fit to a two-
state helix-coil transition model (DG
H2O
= 1.3 ± 0.2 kcalÆmol
)1
;
m = 25 ± 3 kcal mol
)1
ÆM
)1
). Inset: difference spectrum (60–0% TFE)
showing the conformation induced by TFE addition. (C) Interaction
between E7(1-20) andthe RbAB domain, determined using nondena-
turing PAGE. Arrows mark the position of peptides ⁄ complexes:
1 = free peptide, 2 = E7(1-40)–RbAB complex, 3 = E7(1-20)–RbAB
complex. (D) Interaction between E7(1-20) and RbAB in solution.
Experiments were performed at 5 l
M E7(1-20). The titrants
were RbAB (d, K
D
=19±1lM; Table 1), RbAB–E7(16-40) ( , K
D
=
26 ± 1 l
M) and RbAB–E7(1-40) (h, K
D
=30±2lM). A control exper-
iment was performed using 5 l
M FITC-BPVN (4, K
D
> 400 lM).
L. B. Chemes et al. Viraltargetingoftheretinoblastoma protein
FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS 981
phosphorylation is essential for S-phase re-entry of dif-
ferentiating keratinocytes in organotypic raft models
[39,40] and contributes to E7-mediated transformation
[37]. Our results offer the first molecular insight into
the functional role ofE7 phosphorylation, by provid-
ing direct evidence that phosphorylationof serines 31
and 32 of HPV16 E7 increases affinity for the RbAB
domain (Fig. 4). TheE7 region surrounding these resi-
dues is natively unfolded [23] and presents a high den-
sity of negative charge, which may interact with a
conserved lysine-rich patch contiguous to the LxCxE
cleft [41,58]. We showed that phosphorylation affects
the local conformation ofthe E7(16-40) fragment,
increasing the PII content of this region and stabilizing
an extended conformation that optimizes binding to
the LxCxE cleft (Fig. 5). PII-coil transitions induced
by phosphorylation in a similar natively unfolded
PEST region can modulate the stability ofa protein to
intracellular degradation [51], which could also be the
case for theE7 oncoprotein.
The isolated E7 CR1 region is able to bind to the
RbAB domain in vitro with measurable affinity, pos-
sibly undergoing a coil-to-helix transition (Fig. 7). In
the AdE1A protein, the 70-residue spacer between
the CR1 and CR2 regions allows for the simulta-
neous binding of both motifs at opposite sides of the
same RbAB molecule (Fig. 1A,D) [59]. Our data
clearly show that the E7(16-40) and E7(1-40) pep-
tides have the same affinity for the RbAB domain
(Table 1). This result implies that the HPV E7 CR1
region does not contribute to binding when CR2 is
present, which is probably because ofthe short
eight-residue spacer separating both binding motifs.
In a complex between the Rb protein andthe weak
E7 dimer [29], the CR2 region of one E7 molecule
may bind to the LxCxE cleft, while the CR1 region
of the other E7 molecule binds to the E2F site of an
RbAB monomer. This mode of interaction may
cooperate in the displacement of E2F, as previously
suggested [25,27].
Our results highlight the modular nature ofE7 and
its interaction with the RbAB domain (Fig. 8, top). It
has long been recognized that AdE1A and SV40LT
also present multiple interaction modules that bind to
different Rb protein domains [21,22,59]. This is also a
feature ofprototypical Rb protein interacting part-
ners, such as E2F1, HDAC, CtIP and EP300 interact-
ing inhibitor of differentiation 1 (EID-1) (Fig. 8,
bottom). The three secondary sites in E7 (E7C, CR1
and the CKII ⁄ PEST region) contribute far less than
expected from their binding energy in isolation (this
work), which suggests that their main role is to finely
tune affinity and to target multiple interaction sur-
faces ofthe RbAB domain. It will be interesting to
investigate how the action of these modules is inte-
grated with other known E7 interaction sites within
Fig. 8. Interaction modules and affinities ofviraland cellular Rb
protein targets. Proteins and affinities reported are from: HPV-E7
[8,25,34,62] and, from this work, AdE1A [15,43,57], SV40LT
[22,34,56], E2F1 [10,16,18], HDAC [14,34,55], CtIP [13,77] and
EID-1 [9,78,79]. The interaction sites in each protein are marked as
boxes. Linear motifs are marked in color: red (LxCxE motif), dark
blue (CKII site), light blue [cyclin-dependent kinase phosphorylation
(Cdk) site], orange (phosphorylatable serine residues), green (helix
motif), violet (PENF motif) and yellow (FxxxV motif). Dark grey,
interactions mediated by globular domains; light grey, interactions
at unknown sites. Structural domains are indicated above each car-
toon, andthe Rb domains targeted, andthe affinities, are indicated
below each site. When known, the affinities ofthe full-length pro-
teins andthe effects ofphosphorylation are indicated.
Viral targetingoftheretinoblastoma protein L. B. Chemes et al.
982 FEBS Journal 277 (2010) 973–988 ª 2010 The Authors Journal compilation ª 2010 FEBS
[...]... structure oftheretinoblastomatumorsuppressor protein bound to E2F andthe molecular basis of its regulation Proc Natl Acad Sci USA 100, 2363–2368 Dick FA (2007) Structure-function analysis oftheretinoblastomatumorsuppressor protein – is the whole a sum of its parts? Cell Div 2, 26 Lee C, Chang JH, Lee HS & Cho Y (2002) Structural basis for the recognition ofthe E2F transactivation domain bythe retinoblastoma. .. height of each letter within a stack is proportional to its abundance Calculation of conservation scores for surface residues ofthe RbAB domain was carried out using an alignment ofthe RbAB domain from 46 vertebrate species, performed using ClustalW [70] and manual curation Sequences were obtained from PFAM and ENSEMBL [71,72] and from a Psi-Blast search of UNIPROT [73] using thehuman Rb protein as... Fundacion YPF C.S is a recipient ofa University of Buenos Aires predoctoral fellowship I.E.S is the recipient ofa CONICET postdoctoral Viraltargetingoftheretinoblastoma protein fellowship G.d.P.G is a career investigator from CONICET We acknowledge Diana Wetzler for assistance with CD data analysis and Guillermo Solovey for assistance with ProFit programming We thank Liliana Alonso for careful... is the dissociation constant and Po is the total peptide concentration The last term in the equation takes into account slight aggregation that may take place at higher 984 Data analysis We used TFE and GdmCl to stabilize a- helix and PII conformations respectively We assumed that PII populations (for TFE titrations) and a- helix populations (for GdmCl titrations) did not change during titrations, and. .. titrant concentrations, until saturation was achieved The stoichiometry was determined by extrapolation of two linear fits ofthe initial and final anisotropy signals For all reactions tested, full saturation was achieved at a 1 : 1 molar ratio of titrant, indicating a 1 : 1 stoichiometry, which validates the use ofa 1 : 1 binding model (Figs 2B and S2) Binding curves were fit to a model considering a. .. retinoblastomatumorsuppressor Genes Dev 16, 3199–3212 McLaughlin-Drubin ME & Munger K (2009) ThehumanpapillomavirusE7oncoprotein Virology 384, 335–344 Helt AM, Funk JO & Galloway DA (2002) Inactivation of both theretinoblastomatumorsuppressorand p21 bythehumanpapillomavirus type 16 E7oncoprotein is necessary to inhibit cell cycle arrest in human epithelial cells J Virol 76, 10559–10568 Pelka... routes for the prototypic viral oncoprotein: the amyloid-cancer connection Int J Cancer 125, 1902–1911 Uversky VN, Roman A, Oldfield CJ & Dunker AK (2006) Protein intrinsicdisorderandhuman papillomaviruses: increased amount ofdisorder in E6 andE7 oncoproteins from high risk HPVs J Proteome Res 5, 1829–1842 Alonso LG, Garcia-Alai MM, Nadra AD, Lapena AN, Almeida FL, Gualfetti P & Prat-Gay GD (2002)... regions ofthe pRB pocket domain affect its inactivation byhumanpapillomavirusE7 proteins J Virol 76, 6224–6234 Davies RC & Vousden KH (1992) Functional analysis ofhumanpapillomavirus type 16 E7by complementation with adenovirus E 1A mutants J Gen Virol 73, 2135–2139 Liu X & Marmorstein R (2007) Structure oftheretinoblastoma protein bound to adenovirus E 1A reveals the molecular basis for viral oncoprotein. .. identity was confirmed by western blots andby MALDI-TOF MS (Bruker Daltonics, Billerica, MA, USA) Peptide synthesis and labeling Peptides were synthesized at the W M Keck Facility (Yale University, New Haven, CT), and purified by RP-HPLC The phosphorylated E7( 16-40) peptide was obtained by incorporation of phosphoserine, instead of serine, in the synthesis The relative molecular mass of each peptide was confirmed... highlights the complex balance established between physiological and pathological interactions involving the Rb protein [7], and provides essential information towards a better understanding ofthe Rb network of interactions andthe events that determine normal cell cycle regulation or the progression to cell transformation [66] Materials and methods Cloning and protein expression and purification The RbAB . Targeting mechanism of the retinoblastoma tumor
suppressor by a prototypical viral oncoprotein
Structural modularity, intrinsic disorder and phosphorylation. vast importance as the guardian of the cell
cycle and its clinical relevance in human cancers, struc-
tural and thermodynamic understanding of the mecha-
nisms